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Unraveling Genetic Mysteries

Published: Tuesday, August 14, 2012
Last Updated: Tuesday, August 14, 2012
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A UC Berkeley researcher has been awarded $1.3 million of a $3.4 million shared grant to answer some basic scientific questions about inheritance in plants.

Damon Lisch, of the department of Plant and Microbial Biology in the College of Natural Resources, will use the money to continue his research on epigenetic changes in corn -- heritable and functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence. Simply stated, Lisch is interested in changes that take place outside of DNA and that can be passed from parent to child (or in this case the next corn plant).

Exciting Field of Epigenetics

"Scientists love it when rules get broken, and epigenetics breaks a lot of the rules of inheritance, so this field has generated a lot of excitement," Lisch said. He will be carrying out the research with his team, composed of postdoctoral scholars and undergraduate students, near campus, in his lab, and at the Gill Tract in Albany, a field site for researchers affiliated with the College of Natural Resources.

The National Science Foundation grant, announced last week, will enable Lisch and colleagues at other universities to do basic research on epigenetics using maize (corn) as a model organism.

Maize provides an excellent model system for research due to the ease of performing genetic analyses, and the fact that it is a complex genome (an organism's complete set of DNA), and its transposable elements (transposable refers to a DNA sequence that can change its relative position, i.e., self-transpose, within the genome of a single cell).

Transmitting Change

Traditionally, scientists have thought that the inheritance of traits was entirely due to what happened in the DNA sequence, Lisch said.

"However, more recently, we have found that modifications of DNA, and changes in the proteins that DNA is associated with, can also be transmitted from parent to offspring. Unlike changes in DNA sequence, epigenetic changes can be unstable and can be altered by environmental conditions. Thus, experiences that we have may be passed on to our children and even their children because of changes in epigenetic states."

Lisch emphasized that this is important basic research. He is not "trying to make a better corn plant."
"Instead, we are using maize to help us to unravel some basic mysteries concerning the prevalence and importance of epigenetic changes in plants.  Our grant is designed to discover how much epigenetic variation is present in maize, what causes it, and what effects it has on the maize plant. 

With luck, that will tell us a great deal about how plants grow and how they respond to their environment. This is important information if we are to grow enough food for billions of additional people we will have in the next few decades."

"Basic research like this is important because all other research depends on it for fundamental information about how life works, which can have profound implications for more applied research," Lisch said.

To illustrate, Lisch points out that some of the modifications his group has described in corn are similar to those involved in the development of cancer cells and the genetic reprogramming that occurs in stem cells.  Another example is that farmers breed for various traits based on the assumption that they are selecting for particular DNA sequences, but they may also be selecting for epigenetic states that could change depending on environmental conditions.

"More generally, imagine if no one had been studying retroviruses as part of a basic research program before AIDs had come along, or no one had been looking deeply at changes in the climate?  Imagine a world without electronics, which depends on a deep understanding of physics," Lisch said.

The foundation of the grant Lisch received raises the possibility that a memory of environmental or genetic conditions can be encoded and propagated independent of changes in DNA sequence.

The role of epigenetic variation is poorly understood, which is another reason why the National Science Foundation funded the total $3.4 million grant. The grant is shared with:

•    Nathan Springer (Head Principal Investigator on the project) – University of Minnesota
•    Matt Vaughn - Texas Advanced Computing Center at University of Texas, Austin
•    Irina Makarevitch - Hamline University

The genomic datasets from the project will be available to the public and there is an educational component to the grant to provide training and outreach for high school, undergraduate and graduate students.

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